Ropacus_carveme_grampos 
Consistency
This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a formula defined. In steady state, for each metabolite the sum of influx equals the sum of efflux. Hence the net masses of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a formula are not considered to be balanced, even though the remaining metabolites participating in the reaction might be. Implementation: For each reaction that isn't a boundary or biomass reaction check if each metabolite has a non-zero elements attribute and if so calculate if the overall element balance of reactants and products is equal to zero.
A total of 851 (39.51%) reactions are mass unbalanced with at least one of the metabolites not having a formula or the overall mass not equal to 0: DHBZS2H, GLYCL, GLYCL_2, DHBZS3H, CYSTGL_1, ...
This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a charge defined. In steady state, for each metabolite the sum of influx equals the sum of efflux. Hence the net charges of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a charge are not considered to be balanced, even though the remaining metabolites participating in the reaction might be. Implementation: For each reaction that isn't a boundary or biomass reaction check if each metabolite has a non-zero charge attribute and if so calculate if the overall sum of charges of reactants and products is equal to zero.
A total of 0 (0.00%) reactions are charge unbalanced with at least one of the metabolites not having a charge or the overall charge not equal to 0:
Disconnected metabolites are not part of any reaction in the model. They are most likely left-over from the reconstruction process, but may also point to network and knowledge gaps. Implementation: Check for any metabolites of the cobra.Model object with emtpy reaction attribute.
A total of 0 (0.00%) metabolites are not associated with any reaction of the model:
A large fraction of model reactions able to carry unlimited flux under default conditions indicates problems with reaction directionality, missing cofactors, incorrectly defined transport reactions and more. Implementation: Without changing the default constraints run flux variability analysis. From the FVA results identify those reactions that carry flux equal to the model's maximal or minimal flux.
A fraction of 28.88% of the non-blocked reactions (in total 162 reactions) can carry unbounded flux in the default model condition. Unbounded reactions may be involved in thermodynamically infeasible cycles: 4HOXPACt2pp, ABUTt2pp, ABUTt2r, ACACT1r, ACACT2r, ...
The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.
Annotation - Metabolites
The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.
Annotation - Reactions
The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.
Annotation - Genes
The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.
Annotation - SBO Terms
The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.
The Total Score is the result of the following calculation. For more information please click on "Readme" in the top left of the report.
This test reports if the model file is represented in the latest edition (level) of the Systems Biology Markup Language (SBML) which is Level 3, and at least version 1. Implementation: The level and version are parsed directly from the SBML document.